Full information on isolate 1209_contigs (id:73856)
Provenance/primary metadata
- id
- 73856
- isolate
- 1209_contigs
- sender
- Azra Abrar, Khyber Medical University
- curator
- Auto Tagger
- update history
- 2 updates show details
- date entered
- 2024-08-19
- datestamp
- 2024-08-19
- taxonomic designation
- K. pneumoniae
- isolation year
- 2023
- city
- Abbotabad
- country
- Pakistan
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Urine
- infection
- UTI
- source lab
- Microbiology Lab, IPDM, KMU, Peshawar
Publications (3)
- Pubmed id#25278527: No details available.
- Keeling MJ, Danon L, Vernon MC, House TA (2010). Individual identity and movement networks for disease metapopulations. Proc Natl Acad Sci U S A 107:8866-70
- Navarrete F, De La Fuente L (2015). Zinc Detoxification Is Required for Full Virulence and Modification of the Host Leaf Ionome by Xylella fastidiosa. Mol Plant Microbe Interact 28:497-507
Sequence bin
- method
- Illumina
- contigs
- 51
- total length
- 5,389,020 bp
- max length
- 727,651 bp
- mean length
- 105,668 bp
- N50
- 348,838
- L50
- 7
- N90
- 100,598
- L90
- 16
- N95
- 86,406
- L95
- 19
- %GC
- 57.31
- Ns
- 0
- gaps
- 0
- loci tagged
- 697
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| MLST | 7 | 7 | 100 | |
| Ribosomal MLST | 53 | 53 | 100 | |
| scgMLST629_S | 629 | 626 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- YbST
- 304-2LV
- Yersiniabactin
- ybt 13; ICEKp2
- ybtS
- 6
- ybtX
- 4
- ybtQ
- 20
- ybtP
- 61
- ybtA
- 1
- irp2
- 253*
- irp1
- 283*
- ybtU
- 2
- ybtT
- 76
- ybtE
- 4
- fyuA
- 2
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- virulence_score
- 1
- AGly_acquired
- strB.v1*;aph3-Ia.v1^;strA.v1^;aac(6')-Ib-cr.v2
- Flq_acquired
- qnrB1.v2^;aac(6')-Ib-cr.v2
- Sul_acquired
- sul2*
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- OXA-1
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-1^
- spurious_resistance_hits
- catB3.v1?-70%
- resistance_score
- 1
- num_resistance_classes
- 7
- num_resistance_genes
- 11
- Ciprofloxacin_prediction
- nonwildtype R
- Ciprofloxacin_profile_support
- 94.63% R (N=776/820)
- Ciprofloxacin_profile
- 0 QRDR, 1 PMQR, 1 aac(6`)-Ib-cr
- Ciprofloxacin_MIC_prediction
- 2 mg/L [1-2]
- wzi
- wzi137
- K_locus
- KL17
- K_type
- K17
- K_locus_confidence
- Typeable
- K_locus_identity
- 99.96%
- O_locus
- OL2α.1
- O_type
- O1αβ,2α
- O_locus_confidence
- Typeable
- O_locus_identity
- 98.90%
Analysis performed: 2026-01-16; Kleborate v3.2.4
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_89_0_12_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL870
- Clonal group
- CG870
Similar isolates (determined by classification schemes)
Experimental schemes are subject to change and are not a stable part of the nomenclature.
| Classification scheme | Underlying scheme | Clustering method | Mismatch threshold | Status | Group |
|---|---|---|---|---|---|
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 244 (22 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 367 (22 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 244 (22 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 367 (22 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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